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  • Speed of variant callers

    My variant calling seems very slow. What do you think?

    We have 10 BAM files, each about 2.5GB, covering a targetted region of about 15MB.

    I am using the GATK HaplotypeCaller with 8 threads (-nct 8) and it is taking 31 hours.

    When we start whole genome sequencing this will be impossible!

    Any ideas on how to speed things up?

  • #2
    You'll really want to follow Brad Chapman's blog. He writes a lot about various algorithm comparisons and also works on bcbio, which is probably what you're really looking for (see an associated blog post of his here).

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    • #3
      Originally posted by mboursnell View Post
      My variant calling seems very slow. What do you think?

      We have 10 BAM files, each about 2.5GB, covering a targetted region of about 15MB.

      I am using the GATK HaplotypeCaller with 8 threads (-nct 8) and it is taking 31 hours.

      When we start whole genome sequencing this will be impossible!

      Any ideas on how to speed things up?

      The exactSNP is a lot faster. And it has at least comparable performance from our experience.

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      • #4
        OK, thanks. I'll try exactSNP. How did you do the comparison between exactSNP and GATK?

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        • #5
          We are now preparing the manuscript for exactSNP. A preprint should be available early next year.

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          • #6
            If you have pair-end fastq files you can upload them to HiPipe directly (http://hipipe.ncgm.sinica.edu.tw/). HiPipe powered by 640 cores can do alignment (BWA) and variant calling (GATK) very fast. A human exome (70X-100X) can be processed in 2 hrs excluding upload time.

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